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At least 973 records · Page 54Linked to original sources
PubMed1998

Antigenic and genomic analysis of a Borrelia burgdorferi sensu stricto strain isolated from Ixodes ricinus ticks in Alto Adige-South Tyrol, Italy.

A Borrelia burgdorferi sensu lato strain isolated from IXodes ricinus ticks in Alto Adige-South Tyrol (Northern Italy) was analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) of whole cell proteins, Western immunoblotting analysis (WBA) with polyclonal and monoclonal antibodies, and pulsed-field gel electrophoresis (PFGE). The isolate named BZ6 was identified as belonging to the genospecies B. burgdorferi sensu stricto on the basis of its protein profile and its reactivity with monoclonal and polyclonal antibodies. The PFGE study performed with the two rare-cutting restriction enzymes MluI and SmaI confirmed the SDS-PAGE and WBA characterizations, but showed a genetic diversity between the isolate and two out of the three B. burgdorferi sensu stricto strains used in this study as controls, the American type strain B31 and the locally isolated strain BZ1. No difference in the PFGE patterns between the isolate BZ6 and the Swiss strain IRS was noted. Our findings show the value of PFGE analysis for classifying B. burgdorferi sensu lato isolates and for revealing their genetic diversity, and its usefulness for epidemiological investigations.

Animals↗
PubMed2004

Toxicokinetic and genomic analysis of chronic arsenic exposure in multidrug-resistance mdr1a/1b(-/-) double knockout mice.

Multidrug-resistance gene knockout mdr1a/1b(-/-) mice, which are deficient in P-glycoproteins, are more sensitive than wild-type (WT) mice to acute arsenic toxicity. This study assessed toxic manifestations of chronic oral arsenic in mdr1a/1b(-/-) mice, including oxidative stress and altered gene expression, and investigated altered toxicokinetics as a potential basis of enhanced arsenic toxicity. Thus, mdr1a/1b(-/-) and WT mice were exposed to sodium arsenite (0-80 ppm as arsenic) in the drinking water for 10 weeks at which time hepatic arsenic accumulation, lipid peroxidation (LPO), redox status and change in gene expression level were assessed. All mice survived the arsenic exposure, but body weight gain in the highest dose group was reduced in both mdr1a/1b(-/-) and WT mice. Arsenic induced pathological changes, elevated LPO levels and enhanced glutathione S-transferase (GST) activity, in the liver to a greater extent in mdr1a/1b(-/-) than in WT mice. Arsenic also decreased Cu/Zn superoxide dismutase activity in both mdr1a/1b(-/-) and WT mice. The expressions of certain genes, such as those encoding cell proliferation, GST, acute-phase proteins and metabolic enzymes, were modestly altered in arsenic-exposed mice. The expression of cyclin D1, a potential hepatic oncogene, was enhanced in arsenic-exposed mdr1a/1b(-/-) mice only. At the highest level of exposure, hepatic arsenic content was higher in mdr1a/1b(-/-) than in WT mice, suggesting that enhanced accumulation due to transport deficiency may, in part, account for the enhanced toxicity in these mice. In summary, this study shows that chronic arsenic toxicity, including liver pathology and oxidative stress, is enhanced in mdr1a/1b(-/-) mice, possibly due to enhanced accumulation of arsenic as a result of transport system deficiency.

ATP Binding Cassette Transporter, Subfamily B↗
PubMed2004

Genomic analysis reveals RhoC as a potential marker in hepatocellular carcinoma with poor prognosis.

Hepatocellular carcinoma (HCC) is one of the most malignant human tumours because of its high incidence of metastasis. The mechanisms underlying the metastasis of HCC, however, remain poorly understood. In this study, we performed cDNA microarray analysis to profile gene expression patterns in two subtypes of HCC, solitary large HCC (SLHCC) and nodular HCC (NHCC), which differ significantly in the incidence of metastasis. Among 668 genes that were differentially expressed, we focused on RhoC, whose expression was significantly decreased in SLHCC compared to NHCC. The expression of RhoC in HCC and pericarcinomatous liver tissues (PCLT) was analysed at both the mRNA and protein levels by reverse transcription-polymerase chain reaction (RT-PCR) and Western blotting. In addition, immunohistochemistry was also performed on 94 cases of HCC with follow-up information. Collectively, our data indicate that the expression of RhoC significantly increased in HCC compared to PCLT; extrahepatic metastatic lesions expressed significantly higher levels of RhoC than the corresponding intrahepatic HCC tissues. There is a highly significant correlation of the RhoC expression levels with tumour vein invasion, number of tumour nodes and the status of differentiation. Significantly, the HCC patients with RhoC-positive expression had shorter survival than those with RhoC-negative expression. Together, our findings suggest a strong correlation between the expression of RhoC and HCC metastasis, implicating RhoC as a potential prognosis marker and therapeutic target for HCC.

Biomarkers, Tumor↗
PubMed2003

Genomic analysis of Th1-Th2 cytokine genes in an AIDS cohort: identification of IL4 and IL10 haplotypes associated with the disease progression.

Polymorphisms of Th1-Th2 cytokine genes have previously been implicated in the rate of progression to AIDS in seropositive patients. To evaluate further the impact of these genes in the development of AIDS, we have performed an extensive genetic analysis of IL2, IL4, IL6, IL10, IL12p35 and p40, IL13 and IFNgamma. The coding regions and promoters of these genes were sequenced in a Caucasian cohort of 337 HIV-1 seropositive extreme patients (the GRIV cohort) consisting of patients with slow progression and rapid progression, and up to 470 healthy controls. In all, 64 single nucleotide polymorphisms (SNPs) and four deleterious polymorphisms with frequency >1% were identified and evaluated for their association with disease. Statistically significant associations were observed with haplotypes of the IL4 and IL10 genes, but no relation was found with variants of other genes. The catalogue of SNP and haplotypes presented here will facilitate further genetic investigations of Th1-Th2 cytokines in AIDS and other immune-related disorders.

Acquired Immunodeficiency Syndrome↗
PubMedDate not supplied

Comparative genomics analysis of human sequence variation in the UGT1A gene cluster.

Common polymorphisms within the human UGT1A gene locus are associated with irinotecan and tranilast toxicity. To uncover additional functional variation across this gene cluster, cross-species sequence comparisons were performed. Evolutionarily conserved segments (a total of 47.1 kb) were re-sequenced in 24 African-American, 24 European-American, and 24 Asian individuals, and 381 segregating sites (including 123 singletons) were identified. Highly conserved coding sites were less likely to be polymorphic than diverged sites (P<0.0001) but this pattern was not observed at non-coding sites (P=0.1025). Among coding variants, the distribution of those computationally predicted to affect function was skewed toward low frequencies. Some alleles occurred at similar frequencies in each population; others had wide disparities. Although strong linkage disequilibrium was detected among the hepatically expressed genes, the degree of linkage disequilibrium varied among populations. These results suggest that rare functional gene variants and inter-population variability must be considered in the interpretation of association studies between UGT1A and drug metabolism/toxicity phenotypes.

Animals↗
PubMedDate not supplied

Genomic analysis of ABO chimeras and mosaics using hematopoietic colony-derived DNA.

BACKGROUND: While there are many case reports dealing with ABO mosaicism and chimerism, there have been few attempts to determine the patient's genotype. STUDY DESIGN AND METHODS: Peripheral blood and buccal mucosa were obtained from three persons with ABO mosaicism or chimerism. DNA extracted from hematopoietic progenitor cell-derived colonies and from peripheral blood and buccal mucosa were analyzed by polymerase chain reaction-restriction fragment length polymorphism methods. In addition, analyses of short tandem repeat markers were carried out. RESULTS: Hematopoietic progenitor cell-derived DNA analysis revealed that, in two of the three persons there were 2 apparently distinct progenitor cell lineages whose percentages were close to those in the peripheral blood of the patients, as analyzed by flow cytometry; the exception was Subject 3, who had myelodysplastic syndrome (MDS). Short tandem repeat analysis showed that the former two subjects had two pairs of ABO alleles and the latter subject, with MDS, had loss of heterozygosity in some colony-derived DNA as well as blood DNA. CONCLUSION: The subjects without MDS had two distinct hematopoietic cell lineages that led to their ABO chimeric status. The subject with MDS was assumed to have an ABO mosaicism caused by the somatic deletion of the ABO gene in the hematopoietic progenitor cells.

ABO Blood-Group System↗
PubMed1996

Parallel human genome analysis: microarray-based expression monitoring of 1000 genes.

Microarrays containing 1046 human cDNAs of unknown sequence were printed on glass with high-speed robotics. These 1.0-cm2 DNA "chips" were used to quantitatively monitor differential expression of the cognate human genes using a highly sensitive two-color hybridization assay. Array elements that displayed differential expression patterns under given experimental conditions were characterized by sequencing. The identification of known and novel heat shock and phorbol ester-regulated genes in human T cells demonstrates the sensitivity of the assay. Parallel gene analysis with microarrays provides a rapid and efficient method for large-scale human gene discovery.

Cells, Cultured↗
PubMed1999

Genomic analysis of human and mouse TCL1 loci reveals a complex of tightly clustered genes.

TCL1 and TCL1b genes on human chromosome 14q23.1 are activated in T cell leukemias by translocations and inversions at 14q32.1, juxtaposing them to regulatory elements of T cell receptor genes. In this report we present the cloning, mapping, and expression analysis of the human and murine TCL1/Tcl1 locus. In addition to TCL1 and TCL1b, the human locus contains two additional genes, TCL1-neighboring genes (TNG) 1 and 2, encoding proteins of 141 and 110 aa, respectively. Both genes show no homology to any known genes, but their expression profiles are very similar to those of TCL1 and TCL1b. TNG1 and TNG2 also are activated in T cell leukemias with rearrangements at 14q32.1. To aid in the development of a mouse model we also have characterized the murine Tcl1 locus and found five genes homologous to human TCL1b. Tcl1b1-Tcl1b5 proteins range from 117 to 123 aa and are 65-80% similar, but they show only a 30-40% similarity to human TCL1b. All five mouse Tcl1b and murine Tcl1 mRNAs are abundant in mouse oocytes and two-cell embryos but rare in various adult tissues and lymphoid cell lines. These data suggest a similar or complementary function of these proteins in early embryogenesis.

Amino Acid Sequence↗
PubMed2006

Biological assays and genomic analysis reveal lipoic acid modulation of endothelial cell behavior and gene expression.

Lipoic acid (LA) is a sulfated antioxidant produced physiologically as a coenzyme of the pyruvate dehydrogenase complex; it is currently used for treatment of non-insulin-dependent diabetes to favor the cellular uptake of glucose. We have previously described the angiopreventive potential of molecules sharing common features with LA: N-acetyl cysteine, epigallocatechin-3-gallate and xanthohumol. To expand these studies, we have tested the capacity of LA to modulate angiogenesis in tumor growth using a Kaposi's sarcoma model. Endothelial cells exposed to LA displayed a dose-dependent reduction of cell migration and a time-dependent modulation of the phosphorylation of key signaling molecules. In vivo, LA efficiently repressed angiogenesis in matrigel plugs and KS-Imm tumor growth. We analyzed modulation of gene expression in endothelial cells treated with LA for 5 h (early response), finding a mild anti-apoptotic, antioxidant and anti-inflammatory response. A group of LA-targeted genes was selected to perform real-time polymerase chain reaction time-lapse experiments. The long-term gene regulation (48 h and 4 days) shows higher rates of modulation as compared with the array data, confirming that LA is able to switch the regulation of several genes linked to cell survival, inflammation and oxidative stress. LA induced the production of tumor necrosis factor-alpha-related apoptosis-inducing ligand (TRAIL) in KS-Imm and activin-A in KS-Imm and endothelial cells; these factors show anti-angiogenic activity in vivo contributing to explain the inhibitory effect of LA on neovascularization. According to our data, LA has promising anti-angiogenic properties, though its influence on central metabolic pathways should suggest more caution about its widespread and not prescribed use at pharmacological doses.

Anti-Inflammatory Agents↗
PubMed1995

Pulsed-field gel electrophoresis for genomic analysis of Neisseria gonorrhoeae.

Pulsed-field gel electrophoresis (PFGE) is a technique for analyzing large DNA fragments. PFGE was compared to auxotyping and Por serovar (A/S) classification to determine its utility in the study of gonococcal infection, subtyping A/S classes, and clone identification. PFGE patterns were stable in vitro after 2 isolates were passaged 50 times, and those from sex partners were indistinguishable with both enzymes. Fourteen proline-requiring IA-6 isolates from Kenya produced 8 NheI and 7 XbaI patterns; these included 6 Tet M-carrying isolates, all producing the same NheI pattern. PFGE patterns of 14 arginine-, hypoxanthine-, and uracil-requiring IA-1,2 isolates, from the US Pacific Northwest and Hawaii in 1993, were less diverse with both enzymes. PFGE analysis represents a potentially useful addition to the current gonococcal classification system.

Contact Tracing↗
PubMed2026

High-grade astrocytoma with piloid features: a clinical and genomic analysis of prognostic factors using a large cohort.

BACKGROUND: High-grade astrocytoma with piloid features (HGAP) is a recently defined tumor type that is not well-understood. Prognostic factors of clinical outcomes are not well-established. METHODS: Methylation profiling was performed on tumor samples, many at the National Cancer Institute (NCI) Laboratory of Pathology, and others from publicly available sources. Methylation classifier scores of&#x2009;&#x2265;&#x2009;0.90 to the HGAP class on the NCI-Bethesda classifier version 3 were included. Clinical features were collected from the medical record. Survival analyses were performed using the Kaplan-Meier and Cox-proportional hazards methods. RESULTS: The cohort comprised 421 patients. There were high rates of ATRX alteration (62%), CDKN2A/B homozygous loss (78%) and MGMT promoter methylation (53%). MAPK alterations were identified in 74% of evaluable samples. The median age was 46 years, and posterior fossa location was predominant (52%). The median overall survival (OS) was 88 months. Older age (p&#x2009;=&#x2009;0.01) and the presence of an ATRX alteration (p&#x2009;=&#x2009;0.04) were found to be negative prognostic factors. The presence of cystic features on magnetic resonance imaging (MRI) was found to be favorably prognostic (p&#x2009;=&#x2009;0.01). Factors that were not significantly associated with prognosis included histologic high-grade features, CDKN2A/B homozygous deletion, MGMT promoter methylation, extent of resection, and presence of NF1 syndrome. CONCLUSIONS: This large cohort establishes relative frequencies of several important markers. Additionally, older age, the presence of an ATRX alteration, and cystic features on MRI were found to be prognostic. Our work may aid in optimizing treatment regimens for patients with this tumor type.

ATRX alteration↗
PubMed1983

Genomic analysis of antigenically related avian paramyxoviruses.

Six avian paramyxoviruses isolated from wild and domestic ducks in the United States, Hong Kong and Japan were characterized antigenically and genetically. All viruses examined were shown to be antigenically closely related. Oligonucleotide patterns of duck/Miss/334 and duck/Miss/406 were apparently distinguishable from those of duck/Miss/116 and duck/Miss/320 isolated in the same area of the United States. On the other hand, two viruses isolated from a domestic duck in Hong Kong (duck/Hong Kong/D3/75) and from a domestic duck in Japan (duck/Tokyo/41/78) were genetically very similar to that of duck/Miss/116, suggesting that these three viruses represent a genetically homogeneous group and may be of the same origin.

Animals↗
PubMed1985

Genomic analysis of phase I and II Coxiella burnetii with restriction endonucleases.

Restriction endonuclease-digested DNAs from several isolates of phase I and phase II Coxiella burnetii were compared using agarose gel electrophoresis and soft-laser scanning densitometry. Our results demonstrate that the two phases are, as previously assumed, alternative phases of the same organism. Although the restriction endonuclease digestion revealed genetic differences between clonal isolates of phase I and phase II C. burnetii Nine Mile strain, these differences do not appear to be related to antigenic phase variation. However, analyses of the fragment patterns generated by restriction enzyme digestion suggest potential grouping of the different isolates.

Coxiella↗
PubMed2005

Genomic analysis of Hyphomonas neptunium contradicts 16S rRNA gene-based phylogenetic analysis: implications for the taxonomy of the orders 'Rhodobacterales' and Caulobacterales.

Hyphomonas neptunium is a marine prosthecate alpha-proteobacterium currently classified as a member of the order 'Rhodobacterales'. Although this classification is supported by 16S rRNA gene sequence phylogeny, 23S rRNA gene sequence analysis, concatenated ribosomal proteins, HSP70 and EF-Tu phylogenies all support classifying Hyphomonas neptunium as a member of the Caulobacterales instead. The possible reasons why the 16S rRNA gene sequence gives conflicting results in this case are also discussed.

Alphaproteobacteria↗
PubMed2025

Comparative genomic analysis of key oncogenic pathways in hepatocellular carcinoma among diverse populations.

BACKGROUND/OBJECTIVES: Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality, with significant racial and ethnic disparities in incidence, tumor biology, and clinical outcomes. Hispanic/Latino (H/L) patients tend to be diagnosed at younger ages and more advanced stages than Non-Hispanic White (NHW) patients, yet the molecular mechanisms underlying these disparities remain poorly understood. Key oncogenic pathways, including RTK/RAS, TGF-Beta, WNT, PI3K, and TP53, play pivotal roles in tumor progression, treatment resistance, and response to targeted therapies. However, ethnicity-specific alterations within these pathways remain largely unexplored. This study aims to compare pathway-specific mutations in HCC between H/L and NHW patients, assess tumor mutation burden, and identify ethnicity-associated oncogenic drivers using publicly available datasets. Findings from this analysis may inform precision medicine strategies for improving early detection and targeted therapies in underrepresented populations. METHODS: We conducted a bioinformatics analysis using publicly available HCC datasets to assess mutation frequencies in RTK/RAS, TGF-Beta, WNT, PI3K, and TP53 pathway genes. The study included 547 patients, consisting of 69 H/L patients and 478 NHW patients. Patients were stratified by ethnicity (H/L vs. NHW) to evaluate differences in mutation prevalence. Chi-squared tests were used to compare mutation frequencies, while Kaplan-Meier survival analysis assessed overall survival differences associated with pathway-specific alterations in both populations. RESULTS: Significant differences were observed in the RTK/RAS pathway related genes, particularly in FGFR4 mutations, which were more prevalent in H/L patients compared to NHW patients (4.3% vs. 0.6%, p = 0.02). Additionally, IGF1R mutations exhibited borderline significance (7.2% vs. 2.9%, p = 0.07). In the PI3K pathway, INPP4B alterations were more frequent in H/L patients than in NHW patients (4.3% vs. 1%, p = 0.06), while in the TGF-Beta pathway, TGFBR2 mutations were more common in H/L patients (2.9% vs. 0.4%, p = 0.07), suggesting potential ethnicity-specific variations. Survival analysis revealed no significant differences in overall survival between H/L and NHW patients, indicating that molecular alterations alone may not fully explain survival disparities and suggesting a role for additional factors such as immune response, environmental exposures, or access to targeted therapies. CONCLUSIONS: This study provides one of the first ethnicity-focused analyses of key oncogenic pathway alterations in HCC, revealing distinct molecular differences between H/L and NHW patients. The findings suggest that RTK/RAS (FGFR4, IGF1R), PI3K (INPP4B), and TGF-Beta (TGFBR2) pathway alterations may play a distinct role in HCC among H/L patients, while their prognostic significance in NHW patients remains unclear. These insights emphasize the importance of incorporating ethnicity-specific molecular profiling into precision medicine approaches to improve early detection, targeted therapies, and clinical outcomes in HCC, particularly for underrepresented populations.

PI3K pathway↗
PubMed2005

Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana: unique and overlapping functions of ARF7 and ARF19.

The AUXIN RESPONSE FACTOR (ARF) gene family products, together with the AUXIN/INDOLE-3-ACETIC ACID proteins, regulate auxin-mediated transcriptional activation/repression. The biological function(s) of most ARFs is poorly understood. Here, we report the identification and characterization of T-DNA insertion lines for 18 of the 23 ARF gene family members in Arabidopsis thaliana. Most of the lines fail to show an obvious growth phenotype except of the previously identified arf2/hss, arf3/ett, arf5/mp, and arf7/nph4 mutants, suggesting that there are functional redundancies among the ARF proteins. Subsequently, we generated double mutants. arf7 arf19 has a strong auxin-related phenotype not observed in the arf7 and arf19 single mutants, including severely impaired lateral root formation and abnormal gravitropism in both hypocotyl and root. Global gene expression analysis revealed that auxin-induced gene expression is severely impaired in the arf7 single and arf7 arf19 double mutants. For example, the expression of several genes, such as those encoding members of LATERAL ORGAN BOUNDARIES domain proteins and AUXIN-REGULATED GENE INVOLVED IN ORGAN SIZE, are disrupted in the double mutant. The data suggest that the ARF7 and ARF19 proteins play essential roles in auxin-mediated plant development by regulating both unique and partially overlapping sets of target genes. These observations provide molecular insight into the unique and overlapping functions of ARF gene family members in Arabidopsis.

Arabidopsis↗
PubMed1993

HLA-DR, -DQ and -DP alleles in nickel, chromium, and/or cobalt-sensitive individuals: genomic analysis based on restriction fragment length polymorphisms.

The increased concordance rate of nickel sensitivity in monozygotic compared to dizygotic twins indicates a genetic causal component. We have previously described an association in nickel-sensitive subjects with an HLA-DQA restriction fragment length polymorphism (RFLP) (4.5-kb TaqI band, DQA1*0501). The purpose of the present study was to investigate if our previous finding could be confirmed in an independent study, and also to investigate the distribution of HLA class II alleles in chromium- and cobalt-sensitive individuals. Using TaqI- or MspI-digested DNA and DQA, DQB, DRB, DPA and DPB cDNA probes alleles were defined by RFLP analysis. The association with the DQA1*0501 allele was not confirmed in the new group of 37 nickel-sensitive subjects (compared to 150 new controls), nor when the two groups of patients were combined. The distribution of HLA class II alleles and DR-DQ haplotypes were similar in the pooled group of 70 nickel-sensitive subjects and the combined control groups (n = 250). No significant changes in the distribution of HLA class II allele among the chromium- (n = 26) and/or cobalt- (n = 38) sensitive individuals were found. Our results indicate that it is unlikely that the tendency to develop metal sensitivity is associated with alleles of the HLA class II region.

Alleles↗